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Additional file 7: Table S4. Complete list of microbial features (phyla and genera) whose abundance were associated with age (continuous variable) of piglets determined by MaAsLin 2 (Microbiome Multivariable Associations with Linear Models) approach.

Additional file 2: Table S2. Antimicrobial class and concentrations used in agar media to determine bacterial phenotypic resistance.

Additional file 3: Table S3. Metadata and 16S rRNA sequencing read statistics for all samples included in this study.

Additional file 1. Quantification of ARGs in fecal samples from a of cohort of piglets.

Additional file 2: Fig. S1. Non-metric multidimensional scaling (NMDS) ordination plots based on Bray���Curtis distances for (A) used versus (B) unused status for each bedding type, at the phylum, class and ASV level; and for potential mastitis pathogens at the genus level. NSA���new sand, ON���organic non-manure, RMS���recycled manure solids and RSA���recycled sand bedding type. Fig. S2. Log2-fold change (Log2FC) in abundance of classes between used and unused bedding samples, separated by bedding type. Only classes with an average abundance >50th percentile within each bedding type are depicted. Red indicates classes whose abundance was significantly different between used and unused bedding samples (i.e., adjusted P < 0.05). Circle diameter is proportional to the average abundance of each genus across all samples within each bedding type. NSA���new sand, ON���organic non-manure, RMS���recycled manure solids and RSA���recycled sand bedding type. Fig. S3. Log2-fold change (Log2FC) in abundance of genera that contain potential mastitis pathogens, comparing used and unused bedding samples, separated by bedding type. Only genera with an average abundance >50th percentile within each bedding type are depicted. Red indicates genera whose abundance was significantly different between used and unused bedding samples (i.e., adjusted P < 0.05). Circle diameter is proportional to the average abundance of each genus across all samples within each bedding type. NSA���new sand, ON���organic non-manure, RMS���recycled manure solids and RSA���recycled sand bedding type. Fig. S4. Scatter plots of 16S rRNA gene counts and culture results obtained from the same bedding samples, for: total bacteria (panels A���D, TBC); Staphylococcus (panels E���H); 16S rRNA gene counts for Streptococcus and culture-based Streptococcus and Streptococcus like organisms (SSLO) counts (panels I���L); 16S rRNA gene counts for Streptococcus, Aerococcus, Enterococcus and Lactococcus and culture-based Streptococcus and Streptococcus like organisms (SSLO) counts (panels M���P); Bacillus (panels Q���T), and Klebsiella (panels U���X). NSA���new sand, ON���organic non-manure, RMS���recycled manure solids and RSA���recycled sand bedding type.

Additional file 1: Figure S1. Boxplots of the raw sequence read counts by time point and treatment group (Minimal—dark grey, Moderate—blue and Intensive—red color). Horizontal lines forming each box represent the first quartile, median and third quartile, while whiskers denote 1.5x the interquartile range. Figure S2. Proportion of host (Sus scrofa) to non-host reads per sample (x-axis) by treatment groups for each time point. Figure S3. Relative abundance of resistance by type (drugs, biocides, multi-compounds and metals) in composite fecal samples, separated by treatment group (panels) and sampling time point (weaning/transport to market). Figure S4. Microbiome composition (NMDS—non metric multidimensional scaling, Bray-Curtis dissimilarity) at phylum level (stress=0.09) by A) sampling time point (ANOSIM—Analysis of similarities P=0.001, PERMANOVA—Permutational multivariate analysis of variance R2=49%, P=0.001). B) by treatment (ANOSIM P=0.238, PERMANOVA R2

— A highly nutritional protein coding gene AmA1 of Amaranthus hypochondriacus was searched in different species of Amaranthus by using various molecular biological techniques. PCR, Southern hybridization, primed in situ labeling (PRINS) and Cycling-primed in situ labeling (C-PRINS) confirmed the presence of AmA1 coding region only in Amaranthus hypochondriacus. The AmA1 gene was successfully localized on interphase nuclei and also on the metaphase chromosomes. The single copy, unique AmA1 gene was found to be present in the subtelomeric region of two homologous chromosomes in the group of 2-2.2 μm in length. In the present study, a rapid and reliable method for physical localization of single gene on plant chromosome was described and both the methods for in situ localization i.e. PRINS and C-PRINS were compared.